Variant report

Variant	nsv967993
Chromosome Location	chr4:60480224-60496969
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:60481857-60482162	GM12878	blood:	n/a	n/a
2	CTCF	chr4:60481840-60481990	GM12878	blood:	n/a	n/a
3	CTCF	chr4:60481880-60482030	GM12873	blood:	n/a	n/a
4	CTCF	chr4:60481942-60481991	GM19238	blood:	n/a	n/a
5	EP300	chr4:60496523-60497138	T-47D	breast:	n/a	chr4:60497080-60497094 chr4:60496978-60496988 chr4:60497072-60497086 chr4:60497078-60497092
6	EP300	chr4:60494722-60495518	T-47D	breast:	n/a	n/a
7	EP300	chr4:60494943-60495384	T-47D	breast:	n/a	n/a
8	EP300	chr4:60496662-60497025	T-47D	breast:	n/a	chr4:60496978-60496988
9	EP300	chr4:60495857-60496486	T-47D	breast:	n/a	chr4:60496186-60496196 chr4:60496261-60496275
10	ESR1	chr4:60494901-60495355	T-47D	breast:	n/a	n/a
11	ESR1	chr4:60494890-60495330	T-47D	breast:	n/a	n/a
12	ESR1	chr4:60494853-60495407	T-47D	breast:	n/a	n/a
13	ESR1	chr4:60495869-60496362	T-47D	breast:	n/a	n/a
14	FOXA1	chr4:60494786-60495474	T-47D	breast:	n/a	n/a
15	FOXA1	chr4:60496572-60496995	T-47D	breast:	n/a	n/a
16	FOXA1	chr4:60496030-60496384	T-47D	breast:	n/a	chr4:60496181-60496196
17	FOXA1	chr4:60494838-60495429	T-47D	breast:	n/a	n/a
18	FOXA1	chr4:60495847-60496423	T-47D	breast:	n/a	chr4:60496181-60496196
19	FOXA1	chr4:60496561-60496996	T-47D	breast:	n/a	n/a
20	GATA3	chr4:60495844-60496424	T-47D	breast:	n/a	n/a
21	GATA3	chr4:60496713-60497058	MCF-7	breast:	n/a	n/a
22	GATA3	chr4:60495844-60496392	T-47D	breast:	n/a	n/a
23	GATA3	chr4:60496488-60497032	T-47D	breast:	n/a	n/a
24	GATA3	chr4:60494773-60495522	T-47D	breast:	n/a	n/a
25	GATA3	chr4:60494768-60495537	T-47D	breast:	n/a	n/a
26	GATA3	chr4:60496497-60497086	T-47D	breast:	n/a	n/a
27	JUND	chr4:60494835-60495519	T-47D	breast:	n/a	n/a
28	JUND	chr4:60495817-60496414	T-47D	breast:	n/a	n/a
29	JUND	chr4:60496498-60497247	T-47D	breast:	n/a	n/a
30	JUND	chr4:60494803-60495575	T-47D	breast:	n/a	n/a
31	JUND	chr4:60496521-60497188	T-47D	breast:	n/a	n/a
32	JUND	chr4:60495898-60496408	T-47D	breast:	n/a	n/a
33	NRF1	chr4:60487982-60488032	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr4:60488228-60488383	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr4:60495565-60495719	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:60496788-60496888	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr4:60486098-60486280	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr4:60481899-60482051	SK-N-SH_RA	brain:	n/a	n/a
39	SMC3	chr4:60481865-60482117	GM12878	blood:	n/a	chr4:60482002-60482016
40	STAT3	chr4:60495403-60495529	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr4:60496110-60496290	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr4:60489666-60489832	MCF10A-Er-Src	breast:	n/a	n/a
43	STAT3	chr4:60482919-60482953	MCF10A-Er-Src	breast:	n/a	n/a
44	STAT3	chr4:60495333-60495482	MCF10A-Er-Src	breast:	n/a	n/a
45	TCF7L2	chr4:60488918-60489611	PANC-1	pancreas:	n/a	n/a
46	YY1	chr4:60481740-60482112	H1-hESC	embryonic stem cell:	n/a	chr4:60481960-60481968 chr4:60481957-60481979

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:
2	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IGFBP7-7	chr4:60495929-60496042	XLOC_003964

Variant related genes	Relation type
ENSG00000249392	TF binding region
RUNX2	miRNA target sites

Extended variants
information (count: 635 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:635 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565482863	chr4:60480601-60480602	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs532685093	chr4:60480630-60480631	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs184847990	chr4:60480637-60480638	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs151096572	chr4:60480650-60480651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs573298619	chr4:60480685-60480686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs112479515	chr4:60480686-60480687	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs530142394	chr4:60480696-60480697	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs988744	chr4:60480763-60480764	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs569783531	chr4:60480771-60480772	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs189115215	chr4:60480824-60480825	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs549522258	chr4:60480841-60480842	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs558736469	chr4:60480850-60480851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs141034341	chr4:60480900-60480901	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs181010940	chr4:60480920-60480921	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs547295653	chr4:60480956-60480957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs554066069	chr4:60480973-60480974	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs372311144	chr4:60481008-60481009	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs201160975	chr4:60481035-60481036	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs571934066	chr4:60481055-60481056	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs536210795	chr4:60481064-60481065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs577119015	chr4:60481127-60481128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs148238244	chr4:60481134-60481135	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs34250655	chr4:60481185-60481186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs554626697	chr4:60481253-60481254	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs150229274	chr4:60481277-60481278	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs186243134	chr4:60481288-60481289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs191455041	chr4:60481295-60481296	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs577394712	chr4:60481317-60481318	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs113313998	chr4:60481345-60481346	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs538240725	chr4:60481346-60481347	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs530346376	chr4:60481347-60481348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs181445969	chr4:60481370-60481371	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs563350198	chr4:60481385-60481386	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs562792814	chr4:60481386-60481387	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs186076382	chr4:60481403-60481404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs552302428	chr4:60481438-60481439	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs529669836	chr4:60481450-60481451	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs571334164	chr4:60481475-60481476	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs116836922	chr4:60481479-60481480	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs116047759	chr4:60481497-60481498	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs57998071	chr4:60481499-60481500	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs536159528	chr4:60481524-60481525	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554565416	chr4:60481573-60481574	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576152487	chr4:60481650-60481651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs141958842	chr4:60481682-60481683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs145617208	chr4:60481729-60481730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs138140918	chr4:60481730-60481731	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs116519323	chr4:60481761-60481762	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs556886656	chr4:60481786-60481787	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs575035217	chr4:60481789-60481790	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Colorectal cancer	16272173	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16573809	CNVD
Osteoporosis	18992858	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Breast cancer	20369283	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60480600-60481400	Enhancers	Fetal Brain Female	brain
2	chr4:60481200-60481400	Enhancers	Brain Germinal Matrix	brain
3	chr4:60481400-60484200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:60481600-60482200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr4:60481600-60484400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:60482000-60482200	Enhancers	Brain Germinal Matrix	brain
7	chr4:60483200-60483800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:60483400-60483800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:60483400-60484000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr4:60484200-60486800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:60484400-60486800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:60486800-60487400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:60486800-60487400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:60489200-60489600	Enhancers	Liver	Liver
15	chr4:60489600-60495200	Weak transcription	Liver	Liver
16	chr4:60495200-60495600	Enhancers	Liver	Liver
17	chr4:60495600-60495800	Weak transcription	Liver	Liver
18	chr4:60495800-60497000	Enhancers	Liver	Liver

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